Modern Biology Lecture

Nucleic Acids and Protein Synthesis

The first isolation of nucleic acid we now refer to as DNA was accomplished by
Swiss physiologist Johann Friedrich Miescher circa 1870 while studying the nuclei
of white blood cells.

In the 1920's nucleic acids were found to be major components of

chromosomes, small gene-carrying bodies in the nuclei of complex cells.
Elemental analysis of nucleic acids showed the presence of phosphorus, in
addition to the usual C, H, N & O. We now know that nucleic acids are found
throughout a cell, not just in the nucleus, the name nucleic acid is still used for
such materials.

Nucleic Acids

- are unbranched polymers composed of repeating monomers called

nucleotides.
- perform a variety of crucial functions in organisms.

Two Types of Nucleic Acids:

 DNA (Deoxyribonucleic Acid)
- Found within cell nucleus for storing and transfering of genetic
information that are passed from one cell to other during cell
division RNA: Ribonucleic
- stores the genetic information of an organism and transmits that
information from one generation to another.
- gets its name from the sugar molecule contained in its
backbone(deoxyribose); however, it gets its significance from its
unique structure.
- consists of two polynucleotide strands that wind into a right-
handed double helix.

 RNA (Ribonucleic Acid)

- a long unbranched polymer consisting of nucleotides joined by
3′ to 5′ phosphodiester bonds.
- RNA strands consist of from 73 to many thousands of nucleotides.
- translates the genetic information contained in DNA into proteins
needed for all cellular function.
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Nucleotides

Each nucleotide subunit of a nucleic acid contains a phosphate group, a

sugar component, and a heterocyclic ring system (heterocyclic base). The
portion of the nucleotide containing just the sugar and heterocyclic base is
called a nucleoside. Nucleotides are formed from the combination of a sugar
with a phosphate group at the 5′ position and a heterocyclic base at the 1′
position. (′ is used to indicate the carbon number in the sugar to distinguish them
from the atoms in the bases.)

The Heterocyclic Bases

- A ring that contains elements other than carbon is called a heterocyclic

ring.
- The bases found in RNA and DNA contains two types of heterocyclic rings:
pyrimidine and purine.
- pyrimidine bases: uracil (U), thymine (T), cytosine (C)
- purine bases: adenine (A), guanine (G
- DNA contains A, G, T, C; RNA replaces T with U

The Sugar
- In RNA, the sugar component is D-ribose, and in DNA the sugar is D-
deoxyribose. (Note that both sugars are in the b-anomeric form.)
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The Phosphate Group

- The phosphate groups of nucleotides bond to C3' or C5' of the ribose or

deoxyribose rings.
- derived from phosphoric acid, H3PO4 , and at physiological pH exists in
the ionic form:

Polynucleotides

In polynucleotides, nucleotides are joined to one another by covalent

bonds between the phosphate of one and the sugar of another. These linkages
are called phosphodiester linkages. These nucleic acids found in the cell have
primary structures that arise from the end-to-end polymerization of single
nucleotide units. The links between each nucleotide are formed by esterification
reactions between the sugar's C3′ hydroxyl group and the - phosphate of an
incoming nucleoside triphosphate (NTP) to form a phosphoester linkage.

A polynucleotide contains a backbone consisting of alternating sugar and

phosphate groups. The identity and order of the bases distinguish one
polynucleotide from another (primary structure). A polynucleotide has one free
phosphate group at the 5’ end and one free OH group at the 3ʼ end. In DNA, the
sequence of the bases carries the genetic information of the organism.

The Structure of DNA

The Primary Structure of DNA

- DNA is one of the largest molecules known, containing between 1 and

100 million nucleotide units.
- The nucleotides in DNA are linked by phosphate groups that connect the
5′ carbon of one nucleotide to the 3′ carbon of the next.
- Because these connections occur on two oxygen atoms of the
phosphate group, they are called phosphodiester bonds.
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- The nucleic acid backbone then is a sequence of sugar-phosphate

groups, which differ only in the sequence of bases attached to the sugars
along the backbone (the primary structure of DNA)

The DNA Double Helix

- The “ladder-like” structure folds in on itself to form a double helix, with the
bases on the inside and the sugar-phosphate backbone on the outside
- The two intertwined polynucleotide chains run in opposite (antiparallel)
directions, with the 5′ end of one chain on the same side as the 3′ end of
the other.
- The base sequence of a DNA strand is always written from the 5′ end to
the 3′ end.
- The sugar-phosphate backbone runs along the outside of the helix, with
the bases pointing inwards, where they form hydrogen bonds to each
other.
- The two strands of DNA are complementary to each other, because of
the specific pairing of G to C and A to T.

Discovery of the DNA Structure

DNA was discovered in 1869 by the Swiss physician Friedrich Miescher in
the pus of discarded surgical bandages; he named it “nuclein” because it was
located in the nucleus of the cell. In 1878, Albrecht Kossel isolated the pure
nucleic acid, and later isolated the five nitrogenous bases. Many scientists
believed that nucleic acids were far too simple to be the agent that carried
genetic information from one generation to the next, and that the genetic
material would turn out to be a protein. In 1943, Oswald Avery, Colin MacLeod,
and Maclyn McCarty identified DNA as the carrier of genetic information. The
race was on to determine the structure of DNA, and how it was able to transmit
genetic information. In 1952, Rosalind Franklin obtained an X-ray crystal structure
(“Photo 51”) of a sample of DNA which contained structural features which lead
James D. Watson and Francis H. C. Crick to deduce the double helix structure of
DNA (Nobel Prize in Medicine, 1962).

Replication
- the process by which DNA makes a copy of itself when a cell divides.
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- Two strands of DNA separate, and each one serves as the template for
the construction of its own complement, generating new DNA strands
that are exact replicas of the original molecule.
- The two daughter DNA molecules have exactly the same base sequences
of the parent DNA.
- Each daughter contains one strand of the parent and one new strand
that is complementary to the parent strand. This type of replication is
called semiconservative replication.
Steps in DNA Replication
1. Unwinding of the double helix.
- The enzyme helicase catalyzes the separation and unwinding of the
nucleic acid strands at a specific point called a replication fork.
- The hydrogen bonds between the base pairs are broken, and the
bases are exposed.
- An RNA primer attaches to the DNA at the point where replication
begins.
2. Synthesis of DNA Segments.
- DNA replication takes place from the 3′ end towards the 5′ end of
the exposed strands (the template).
- Because the strands are antiparallel, the synthesis of new nucleic
acid strands proceeds:
• toward the replication fork on one strand (the leading
strand)
• away from the replication fork on the other strand (the
lagging strand).
- Nucleotides complementary to the ones on the exposed strands
are attached to the growing chain, and are linked together by the
enzyme DNA polymerase to form a new daughter strand.
3. Closing the Nicks.
- The daughter strand along the leading strand is synthesized
smoothly, without any nicks.
- The Okazaki fragments along the lagging strand are joined by an
enzyme called DNA ligase, which removes the RNA primer and
replaces it with the correct nucleotides.
- The result is two DNA double-helix molecules of DNA that are
identical to the original DNA molecule, each of which contains one
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old strand from the parent DNA and one new daughter strand
(semiconservative replication).

Types of RNA
 Messenger RNA (mRNA)
- functions as a carrier of genetic information from the DNA in the cell
nucleus to the site of protein synthesis in the cytoplasm.
- The bases of mRNA are in a complementary sequence to the base
sequence of one of the strands of nuclear DNA.
- mRNA has a short lifetime (usually less than one hour); it is
synthesized as it is needed, then rapidly degraded to the
constituent nucleotides.
 Ribosomal RNA (rRNA)
- the main component of ribosomes that are the site of protein
synthesis.
- rRNA accounts for 80-85% of the total RNA of the cell.
- rRNA accounts for 65% of a ribosome’s structure (the remaining 35%
is protein).
- provides the site where polypeptides are assembled during protein
synthesis.
 Transfer RNA (rRNA)
- brings specific amino acids to the ribosomes for protein synthesis.
- tRNA is specific to one type of amino acid; cells contain at least
one specific type of tRNA for each of the 20 common amino acids.
- tRNA is the smallest of the nucleic acids, with 73-93 nucleotides per
chain.
- tRNA has regions of hydrogen bonding between complementary
base pairs, separated by loops where there is no hydrogen
bonding.
- Two regions of tRNA have important functions:
 the anticodon is a three-base sequence which allows
tRNA to bind to mRNA during protein synthesis. (It is
complementary to one of the codons in mRNA.)
 the 3′ end of the molecule binds to an amino acid with
an ester bond and transports it to the site of protein
synthesis. An enzyme matches the tRNA molecule to
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the correct amino acid, “activating” it for protein

synthesis.
 tRNA is drawn as a cloverleaf shape, with an acceptor stem at the
3ʼ end, which carries the needed amino acid, and an anticodon,
which identifies the needed amino acid.
Parts of Protein Synthesis
 Transcription
Before the synthesis of a protein begins, the corresponding RNA
molecule is produced by RNA transcription. One strand of the DNA double helix
is used as a template by the RNA polymerase to synthesize a messenger RNA
(mRNA). This mRNA migrates from the nucleus to the cytoplasm. During this step,
mRNA goes through different types of maturation including one 8 called splicing
when the non-coding sequences are eliminated. The coding mRNA sequence
can be described as a unit of three nucleotides called a codon. Transcription is
the synthesis of mRNA from DNA. The DNA splits into two strands, the template
strand, which is used to synthesize RNA, and the informational strand which is not
used. Transcription proceeds from the 3ʼ end to the 5ʼ end of the template.
Transcription forms a mRNA with a complementary sequence to the template
DNA strand and an exact sequence as the informational DNA strand. The
difference between mRNA and the information DNA strand is that the base U
replaces T on mRNA. Transcription is the ordered synthesis of RNA from DNA; the
genetic information stored in DNA is passed onto RNA. In eukaryotes, the DNA
containing the stored information is in the nucleus of the cell, and protein
synthesis occurs in the cytoplasm. The information stored in the DNA must be
carried out of the nucleus by mRNA.
 Translation
Translation is the synthesis of proteins from RNA; the genetic
information determined the specific amino acid sequence of the protein.
The ribosome binds to the mRNA at the start codon (AUG) that is
recognized only by the initiator tRNA. The ribosome proceeds to the
elongation phase of protein synthesis. During this stage, complexes,
composed of an amino acid linked to tRNA, sequentially bind to the
appropriate codon in mRNA by forming complementary base pairs with
the tRNA anticodon. The ribosome moves from codon to codon along the
mRNA. Amino acids are added one by one, translated into polypeptidic
sequences dictated by DNA and represented by mRNA. At the end, a
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release factor binds to the stop codon, terminating translation and

releasing the complete polypeptide from the ribosome. One specific
amino acid can correspond to more than one codon. The genetic code
is said to be degenerate. mRNA serves as a template on which amino
acids are assembled in the sequence necessary to produce the correct
protein. The code carried by mRNA is translated into an amino acid
sequence by tRNA.
Steps of Translation
 Initiation
 The small subunit of the ribosome binds to a site
"upstream" (on the 5' side) of the start of the
message.
 mRNA and a small ribosomal subunit join; the
initiating codon (AUG) is aligned with P (peptidyl)
site of the subunit.
 tRNA brings in methionine (eukaryotes) or N-
formylmethionine (prokaryotes).
 The resulting complex binds to the large
ribosomal subunit to form a unit called the
initiation complex.
 begins with mRNA binding to the ribosome.
 Elongation
 The next incoming tRNA with an anticodon that is
complementary to the mRNA codon bonds at
the A (aminoacyl) site on the mRNA.
 A peptide bond is formed between the amino
acid segments, (catalyzed by peptidyl
transferase), which releases the amino acid
chain from the P site.
 The “empty” tRNA released, and the whole
ribosome moves one codon along the mRNA
towards the 3’ end (translocation).
 Another tRNA attaches to the A site, and the
elongation process is repeated.
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 proceeds as the next tRNA molecule delivers the

next amino acid, and a peptide bond forms
between the two amino acids.
 Termination
 Elongation continues until the ribosome complex
reaches a stop codon (UAA, UAG, or UGA).
 A termination factor protein binds to the stop
codon, and separates the protein from the final
tRNA.
 The ribosome can then synthesize another
protein molecule.
Transcription: RNA Synthesis
Transcription is the process of creating an equivalent RNA copy of a
sequence of DNA in double helix. Both RNA and DNA have base pairs of
nucleotides as a complementary language that can be converted back and
forth from DNA to RNA in the presence of the correct enzymes, RNA polymerase.
During transcription, a DNA sequence is read by RNA polymerase, which
produces a complementary, antiparallel RNA strand. As opposed to DNA
replication, transcription results in an RNA complement that includes uracil (U) in
all instances where thymine (T) would have occurred in a DNA complement.

Transcription is the first step leading to gene expression. The stretch of DNA
transcribed into an RNA molecule is called a transcription unit and encodes at
least one gene. If the gene transcribed encodes for a protein, the result of
transcription is messenger RNA (mRNA), which will then be used to create that
protein via the process of translation. Alternatively, the transcribed gene may
encode for either ribosomal RNA (rRNA) or transfer RNA (tRNA), other
components of the protein-assembly process, or other ribozymes.

A DNA transcription unit encoding for a protein contains not only the
sequence that will eventually be directly translated into the protein (the coding
sequence) but also regulatory sequences that direct and regulate the synthesis
of that protein. The regulatory sequence before (upstream from) the coding
sequence is called the five prime untranslated region (5'UTR), and the sequence
following (downstream from) the coding sequence is called the three prime
untranslated region (3'UTR). 10 Transcription has some proofreading
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mechanisms, but they are fewer and less effective than the controls for copying
DNA; therefore, transcription has a lower copying fidelity than DNA replication.
As in DNA replication, DNA is read from 3' → 5' during transcription.
Meanwhile, the complementary RNA is created from the 5' → 3' direction.
Although DNA is arranged as two antiparallel strands in a double helix, only one
of the two DNA strands, called the template strand, is used for transcription. This
is because RNA is only single-stranded, as opposed to double-stranded DNA.
The other DNA strand is called the coding strand, because its sequence is the
same as the newly created RNA transcript (except for the substitution of uracil
for thymine). The use of only the 3' → 5' strand eliminates the need for the
Okazaki fragments seen in DNA replication.Transcription is divided into 5 stages:
pre-initiation, initiation, promoter clearance, elongation and termination.

Splicing of mRNA: Splicing is a modification of an RNA after transcription, in

which introns (nonessential part opf the code)are removed and exons(essential
part opf the code) are joined. Also tThe UTRs, non-coding parts of exons at the
ends of the mRNA is also removed.

Codon: The code is defined as a mapping of three-nucleotide base sequences

and the amino acids. A triplet codon in a nucleic acid sequence usually
specifies a single amino acid (though in some cases the same codon triplet in
different locations can code unambiguously for two different amino acids.

Genetic Code
- The communicative relationship between mRNA nucleotides and
amino acids in a protein.

Once the 3D structure of DNA was known, it was clear that the sequence
of the bases along the backbone in some way directed the order in which
amino acids were stacked to make proteins. In 1961, Marshall Nirenberg and his
coworkers began to unravel the connection between the base sequence in
DNA and the amino acid sequence in proteins. The genetic code uses a
sequence of three bases (a triplet code) to specify each amino acid. (A triplet
code gives 43=64 possible combinations, which is more than enough to specify
the 20 amino acids.) Each base triplet sequence that represents a code word
on mRNA molecules is called a codon.
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DNA code: containing specific base code to create a specific polypepetidethe

protein containing a certain sequence of amino acids.

The genetic code consists of 64 triplets of nucleotides. These triplets are

called codons. With three exceptions, each codon encodes for one of the 20
amino acids used in the synthesis of proteins. That produces some redundancy
in the code: most of the amino acids being encoded by more than one codon.

Genetic Code: mRNA Codons for each of the 20 Amino Acids

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Characteristics of the Genetic Code

- The genetic code applies almost universally: with minor exceptions,

the same amino acid is represented by the same codon(s) in all
species.
- Most amino acids are represented by more than one codon (a
feature known as degeneracy).
– Only methionine and tryptophan are represented by a
single codon.
– Leucine, serine, and arginine are represented by six codons.
– No codon codes for more than one amino acid.
- Only 61 of the 64 possible triplets represent amino acids. The other
three are used as signals for chain termination (a “stop” signal).
- The AUG codon (which also codes for methionine) functions as a
“start” signal, but only when it occurs as the first codon in a
sequence.

Genetic Mutation
- Mutations are any changes resulting in an incorrect base sequence on
DNA.
- Even though the base-pairing mechanism provides a nearly perfect way
of copying DNA, on average one out of every 1010 bases are copied
incorrectly.
– This leads to a change in the amino acid sequence in a protein, or
causes the protein not to be made at all.
- Mutations occur naturally during replication. They can also be induced by
environmental factors:
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– ionizing radiation (X-rays, UV, gamma rays).

– mutagens, which are chemical agents.
- Mutations may be beneficial to an organism by making it more capable
of surviving in its environment, ultimately (over millions of years of
accumulating changes) leading to the evolution of new species.
- Since much of an organisms DNA does not code for anything, mutations
in these regions are neutral.
- Other mutations can be harmful, either producing genetic diseases or
other debilitating conditions.

Point Mutation
- substitution of one nucleotide for another.

Deletion Mutation
- occurs when one or more nucleotides is/are lost from a DNA molecule.

Insertion Mutation
- occurs when one or more nucleotides is/are added to a DNA molecule.
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Silent Mutation
- has a negligible effect to the organism, because the resulting amino acid

is identical.